Cilia and centrioles are evolutionarily conserved eukaryotic organelles. Cilia sense the environment through a growing list of ciliary membrane localized receptors and proteins and/or move cells or fluids. Centrioles are also microtubule-based organelles that perform several functions. A centriole is matured into a basal body, which functions as a platform for templating/anchoring cilia to the membrane. Centrioles organize both cytoplasmic and spindle microtubules. During maturation of centrioles, a distal structure known as the transition zone is assembled. It consists of morphologically defined structures known as transition fibers, the Y- linkers, and the membrane-embedded ciliary necklace. Little is known about how the ciliary necklace is assembled onto the Y-linkers, or how the transition zone serves as a barrier between the cytoplasm and cilia. Many of the human ciliopathies affect proteins in the transition zone. Our newly discovered cnc1 mutant lacks the ciliary necklace, but has transition fibers and the Y- linkers. The cnc1 mutant provides a unique tool to dissect how proteins are assembled into the ciliary necklace, the identify of these ciliary necklace proteins and the role of this structure. Mutations in the Nek1 kinase cause retinal degeneration and abnormal bone growth in patients. Our analysis of the Nek1 homolog in Chlamydomonas suggests that it affects the transition zone, IFT regulation, and spindle microtubules. Analysis of its targets in the basal body and flagella as well as interacting proteins will help to dissect the role of this conserved kinase in ciliary and microtubule biology. Using electron tomography, our recent finding that the duplication of new centrioles initiates at a particular triplet microtubuleon the old centriole is really exciting, and we would like to know what molecules mark this site. Centrioles are built of triplet microtubules, but few proteins that affect triplet microtubule assembly are known. To address these and other questions, an unbiased forward genetic screen for new basal body duplication defective mutants together with whole genome sequencing and light and electron microscopy will identify the roles of new proteins in these two important events. In addition, the mutants from the genetic screen will be used to ask if there are assembly factors that are needed for centriole duplication, but are not structural components of centrioles.